Gray Days
by gatewatcher
Summary: There seems to be a misunderstanding in the newly changed relationship between Booth and Brennan. Rated T just to be on the safe side.
1. Chapter 1

This story takes place during Season 6. It begins after "Hole in the Heart" but before Angela gives birth. It's a bit AU as the case at the bowling alley won't happen and Booth finds out about Brennan's pregnancy in a different manner.

As always, "Bones" isn't mine. I'm just playing and will put them up nicely when I'm done. 😊

Please let me know what you think. Gatewatcher

Ch 1

The day was gray. Early spring days can often be chilly and it takes the sun a while to decide to appear in the morning. While most people were still sleeping, snuggled underneath warm blankets, Brennan was already in the lab working on identifying the many bodies that came to her three weeks ago. As usual, she spent every waking hour in the lab working. She wasn't even sure when she ate last. Several weeks ago, she had thought things were changing. After the death of her English intern, Vincent Nigel-Murray, she and Booth had become even closer than they ever had been before. She had stayed at Booth's apartment that night. At first, she had considered having to stay there unnecessary, but he needed to be sure she was not in harm's way with Broadsky still on the loose, so she acquiesced and stayed to make Booth feel better. She had realized later that he knew she would end up needing him, allowing him/asking him to hold her as she lost all control of her emotions from the loss of such a young life. Since that night, they had barely been separated; that included work hours and after hours. Some nights she spent at his apartment, and some nights he stayed at hers. Right now, though, if she were to compare how she felt to a color, it would be gray, same as the dawning day.

Three weeks ago, on a Monday morning, she had come into work late. She had an early appointment and entered the lab about nine o'clock. Booth had spent the night at her place, but they drove in separately. She had barely gotten busy when her phone buzzed.

"Brennan", she announced as she answered the call.

"Bones, it's me. I'm headed over to get ya."

"Where are we going?"

"I'll explain on the way."

Ten minutes later, the pair was on their way to Jamestown, Virginia. Booth had explained that a construction company was digging to begin on a new project when they discovered a mass grave site.

"Apparently", he had informed her, "the bodies appear to be very old; there are no decayed coffins, grave markers, or anything like that anyone has been able to decipher. So, they asked for you and the team to take a look at it."

Arriving on scene, Brennan grabbed her gear and met with the FBI forensics team. As she stepped down into the massive hole in the ground where they construction crew had been digging, she observed several sets of bones. Most were just lying in the dirt. The bodies weren't all intact.

She yelled up to Booth, "These are old; probably nearly 100 years."

He reached out for her hand to assist her out of the hole as she continued to speak. "We would have to excavate them all out and try to match sets together to make individual remains. It will take quite a while. They were correct in stating there are no coffins. It appears to be a large body dump."

"Okay, let's call Hodgins and Cam and get the team down here. You guys can start digging it all out and get this party started."

"Booth. This will hardly be a party", she exclaimed as she pulled out her phone.

Booth just shook his head and turned around to go find the construction supervisor.

Toward the end of the week, Brennan and Hodgins were nearly finished with sifting through the dirt for remains. She was just about or ask for a large amount of the soil to be trucked to the Jeffersonian when a news crew pulled into the lot.

Booth headed over to the van to try and intercept them. He walked up to the back of the van as the crew was taking out their equipment.

"Excuse me. I'm Special Agent Booth from the FBI. I'm sorry, but you can't…"

"Hello, Seeley", cooed the blonde as she turned around to face him.

"Hannah? What are you doing here?"

"Trying to get a story, Seeley. My job."

"I thought you were….."

"I am waiting for a transfer back to Afghanistan; it just hasn't come through yet."

"I see."

"Come on, Troy. Let's go get some footage and see if we can get anyone to talk to us" she ordered as she by-passed Booth with her eye on the large hole in the ground.

Brennan had been watching from across the lot as Booth and Hannah spoke. She made an assumption that this was the first they had spoken since she turned down his marriage proposal.

Hannah strode straight toward Brennan with her cameraman right behind her.

"Hello, Temperance."

"Hello, Hannah."

Hannah then turned to the cameraman and motioned for him to start filming and then began…

"Good afternoon. This is Hannah Burley with WHDC and we are in Jamestown, Virginia where we have been told that crews discovered a mass burial site. I am with the world's most renowned forensic anthropologist, Dr. Temperance Brennan from the Jeffersonian Institute. Dr. Brennan, what can you tell us about what you have found here? Could this be the people from a mass murder, a Native American tribe, or perhaps a lost colony? Then she thrust the microphone into Brennean's face.

"I have no idea", she responded indignantly. "How could I know what this is until I get it all back to the lab and have time to study it?"

"Well, could you at least give our viewers an educated guess? What do you think this is?"

"I do not speculate nor do I guess. I must review the remains to obtain facts. You should know that, Hannah", she replied as she turned and walked away.

Hannah tried to speak with Jack and then to a security detail, but no one would give her any information. Sighing, she instructed the cameraman to call it a day and begin putting the equipment back into the van.

The whole time she was trying to get a story out of this, Booth just watched and shook his head.

While Troy was putting things away, Hannah walked over to Booth and began a conversation.

Brennan observed from a distance wondering what they were discussing when her phone rang.

"Brennan. Yes. Yes. I will. Thank you for your call." She began to mentally make plans for dinner. When she looked up from replacing her phone, Booth was coming toward her.

"Bones", he shouted. "Are you ready to pack up and get out of here?"

"You don't have to shout, Booth. Yes, I believe we have all that we need for now."

As they started to walk to his SUV, Hannah ran back towards him and asked if they could have dinner together.

He started to say no, when she pleaded with him to have a chance to talk. He turned to look at Brennan. They hadn't informed anyone yet that they had started a relationship, and this was not the way they wanted their friends to find out. She smiled and stated that perhaps it was a good idea if they clear the air.

"I will be working on these remains. You may as well go and have dinner. Bring me something back."

So, he agreed to meet Hannah at Founding Father's at 6:00 after dropping Brennan off at the lab.

That was the last time she had seen Booth. That was two weeks ago. He called her at 8:00 that evening and said that he had to go out of town for a few days. He said he would call her when he returned and not to worry. He also told her that Agent Barrett would be taking his place and was looking into the area where they discovered the bodies. Before he hung up, she overheard a female voice say, "Come on Seeley. We'll miss the flight." And she hasn't heard anything since.

So, she has spent every day, and most nights, working on the remains. In that amount of time, she had put together nearly a dozen bodies and identified eight of them. As it turns out, in the early 1900's, an asylum had stood on the ground where the bodies were found. It had been abandoned an eventually demolished in 1942. The remains they found had been patients who had died while in residence, mostly from illnesses. There was no foul play that she could decipher; she was having them returned to family members or arranging for proper burials.

Eventually, on this early gray morning, Jack and Angela arrived and found her working. As Angela watched her, she whispered to Jack that Brennan was looking very pale. She marched over to her and demanded that she stop working for a while.

"Bren, come on. I'm hungry. Let's go to the diner and get some breakfast."

"You only just arrived. How can you be hungry already?"

"Well, this baby is hungry all the time. I always want to eat", she smiled. "When's the last time you ate?"

Brennan just looked at her.

"Ahuh. That's what I thought. Come on. No arguments. Let's go."

"Ang….."

"Nope. Jack, help me."

"Come on Dr. B. Humor her. It's useless to argue."

"Fine." Taking off her lab coat, she was going to hang it in her office. She turned quickly and took a step. Immediately feeling light headed, she lost her balance and nearly fell down the steps. Luckily, Jack was only a few feet away and managed to catch her before her unconscious body hit the floor.


	2. Chapter 2

Author's note: Thank you all so much for the very nice reviews! I appreciate your time, the Follows, and the Favorites. I believe I have responded to the ones I could. To my guests, thank you all as well. I hope you continue to enjoy.

Ch 2

Two weeks ago—Booth's POV

"Bones", he shouted. "Are you ready to pack up and get out of here?"

"You don't have to shout, Booth. Yes, I believe we have all that we need for now."

As they started to walk to his SUV, Hannah ran back towards him and asked if they could have dinner together.

He started to say no, when she pleaded with him to have a chance to talk. He turned to look at Brennan. They hadn't informed anyone yet that they had started a relationship, and this was not the way they wanted their friends to find out. She smiled and stated that perhaps it was a good idea if they clear the air.

"I will be working on these remains. You may as well go and have dinner. Bring me something back."

So, he agreed to meet Hannah at Founding Fathers at 6:00 after dropping Brennan off at the lab.

Pulling up in front of the Jeffersonian, Booth stopped the SUV and placed it in park.

"Bones, are you sure about me having dinner with Hannah and not you?"

"I trust you, Booth. I will be working on the remains. You may as well have dinner. I will see you this evening."

"Okay. I will come here after dinner. I love you."

"I love you too." She then leaned in towards him as they kissed and she left the vehicle.

Before he could turn the SUV around to head towards the Founding Fathers, his phone chirped. Picking it up, he answered it, "Booth. Yes, sir. I'm on my way."

Fifteen minutes later, he walked into Director Stark's office. The secretary waived him in simply stating, "He's expecting you."

Entering the room, he was surprised to see his friend Danny Beck from the CIA sitting in front of the director's desk.

"Danny? What's up?"

Danny just answered him with a nod and "Booth."

"Agent Booth, the CIA has requested to borrow you for a special operative assignment and the bureau has agreed to their request."

"But, sir, I am in the middle of an investigation with Dr. Brennan."

"Don't worry, I will be assigning Agent Barrett to work with Dr. Brennan and take over the case."

"Sir, I really…"

"The decision has been made, Booth. Go home and pack a light bag. Agent Beck will fill you in on the way to your destination."

"I don't even get to know where I'm headed?"

"Not until you're in the air."

"Right. I'd like to call Dr. Brennan before I leave, sir. After the last time I disappeared, and she thought I was dead, well, I would like to prevent that from happening again."

"You cannot give her any details at all."

"I don't know any that I could give her anyway, but at least she'll know I'm all right."

"Very well then. One quick call."

"Thank you, sir."

After that, Booth cancelled his dinner with Hannah, went home to pack a bag, and took a cab to the airport.

While waiting, he ran into Hannah who was given her transfer back to Afghanistan. He discovered that she would be hitching a ride on the same plane that he and Danny would be on. He finally took a moment to call Brennan to let her know he was going to be out of town for a few days when Hannah called for him to board.

That was two weeks ago. Today, he was so glad to finally be home. The op took much longer than anticipated. As he exited the plane, he thought to himself, _'Danny is going to owe me big for this one_.' Noting the dull grayness of the day, he compared it to the way he'd been feeling over the last fourteen days. He was so looking forward to that improving as his day went on. With that thought, he left the airport and took a cab to his apartment where he showered, changed into comfortable clothing, and then took off to find his Bones.


	3. Chapter 3

Thank you again for the wonderful reviews. I decided to go ahead and post Ch 3 :)

Ch 3

About noon, Booth came striding through the glass doors at the Jeffersonian. He had already been to Brennan's apartment, but not finding her car in the lot, he decided that he should have known she would be at work. Entering her office, he noted she wasn't there. Continuing into Angela's office, into Hodgins', Cam's, and even into limbo, he found no one. Finally, he grabbed his phone from his pocket and hit Speed dial #1.

Feeling the phone vibrate in her pocket, she picked it up and answered, "Brennan's phone".

"Ang…."

"Booth! Oh, my God, where have you been? Do you know she's worked herself crazy!? How could you just disappear like that and not call, nothing….."

"Angela, put Bones on the phone please." He didn't have the patience to be lectured by Brennan's well-meaning best friend.

"I can't."

"Come on, Ang. Let me talk to Bones. Why are you answering her phone in the first place?"

"Booth, we're at the emergency room at George Washington."

"Are you having the baby?"

"No, Booth. It's Brennan; she collapsed this morning and we brought her here ."

"I'm on my way!" and with that he ended the call and ran out of the lab as fast as he could. Using his siren, he sped through city traffic. Throwing it into park, he jumped from his SUV and hustled to the entrance to the ER and found not only Angela, but Hodgins and Cam in the waiting area.

"What happened?"

"She's been working non-stop with these bodies from the mass grave site", Angela began. I have only been working half days for the last week or so and hadn't realized how much time she was really spending at the lab."

Jack interrupted and stated, "Angie, this isn't your fault."

"So, ….."

Jack added, "When we came in this morning, she was already working. We noticed how pale she was and Angie talked her into stopping and we were taking her to eat. She took off her lab coat, turned around, and passed out."

"Jack caught her just before she hit the floor."

"How is she?"

Cam entered the conversation stating, "We haven't heard anything from the doctor yet. We're still waiting."

A few moments later, the doors opened and a female doctor came through and called, "Family of Temperance Brennan."

The foursome stepped up.

"Is there a Seeley Booth here?" the doctor inquired.

"I'm Booth."

"I am Dr. Couch. You are listed as Temperance's medical proxy; is that correct?"

"Yes. Is she okay?"

"Temperance is suffering from exhaustion and she is severely dehydrated, but she will be fine. We are giving her an IV of liquids. With that and some rest, she should feel more herself in a couple of days. We are going to keep her overnight for observation, but she should be able to go home in the morning."

"Can we see her?"

"Of course. They are cleaning her up after the sonogram and will be moving her to room 447 on the fourth floor."

Angela asked, "What was the sonogram for? Did she injure something when she fell?"

The doctor replied, "No. We were just making sure that everything was fine with the baby. You may head up to 447 at any time."

With that, four sets of eyes blinked and stared at the retreating woman.

After she walked back through the set of double doors, they all looked at each other.

"What?", asked Angela.

"Baby?", repeated Jack.

"Did she say what I thought she said?" asked Cam.

The only one that didn't say anything was Booth. He just backed up and sat down on the nearest chair.

"Booth?" said Angela looking at him. "Did you know…?"

Shaking his head, he said, "No."

Looking at the shock on his face, Angie announced quietly, "You're the father… aren't you?"

Clearing his throat and looking at his friends, he shook his head, "Yea."

More shock was now on Cam's face. "Wha….? When?"

"Cam, we didn't tell anyone about our relationship because…."

"But you didn't know about the baby?"

"No."

"Where have you been, man?" asked Jack.

"I can't tell you."

Angela said, "OK. You can pull that ' _can't tell FBI stuff_ ' with us, big guy; but you're going to have to do better than that with Bren. You need to tell her whatever you did and why you were gone for so long. She was really worried ya know."

"Yea. I need to go talk to her. Listen. I know you guys brought her here and you're worried about her, too, but would you mind if I went up right now by myself? Can you give us some time?"

"Yes. Come on you two. Let's go. We'll come back later, Seeley", stated Cam.

"But…." countered Angela.

Jack jumped in, "Let's go eat. We'll be back later."

She didn't want to go, but she shook her head, "All right, we'll go. You go make this right."

Booth just shook his head.

"Give her a hug for me, please."

And with that, Booth watched the three of them head toward the exit. Taking a deep breath and rubbing the back of his head, he turned and headed toward the elevator.

A.N. Well, this chapter answered one question. I hope it didn't disappoint.


	4. Chapter 4

This is the last of the story. School starts next week and I have to start writing lesson plans instead. Thanks for reading :)

Ch 4

Booth took the elevator to the fourth floor. He found his way to room 447 and saw that Brennan was already set up there. No one else was in the room. For a moment, he just stood there, staring at her. _'God, she's beautiful'_ , he thought. He didn't care that she was wearing a hospital gown. He noted that she **was** very pale and looked very tired. She had her head down giving all her attention to a piece of paper that she held in her hand. Putting on a smile, he decided it was time to go in. Not wanting to startle her, he knocked on the door and then stepped in.

"Hey, Bones. How ya feelin'?"

She looked up when she heard the knock and surprise was written all over her face. She couldn't believe Booth was the person entering the room. She expected Angela, but not Booth, so she lay there speechless, not knowing what to say.

Her surprised look soon turned into one of anger. She placed the paper she was holding on the bedside table, still not saying a word.

"Hey, I'm sorry."

She managed to choke out, "For what, Booth? For what are you sorry?"

"I'm sorry I pulled a disappearing act."

"Where were you?" she inquired, swallowing hard and still not looking at him.

Booth walked up to the bed and stood next to her. "I was in Afghanistan", he said softly.

"Why?"

"I really can't tell you why I was there."

Blinking, trying not to allow tears to fall, she asked, "How is Hannah?"

With a confused look on his face, he asked, "Why would you ask about Hannah?"

"When you called me to say you were leaving, you were traveling with Hannah. I heard her voice tell you that you were about to miss your flight."

Thinking back to the day he left, it dawned on him what was going on. Shaking his head 'no', he grabbed her hand into both of his and repeated, "No, no, no, no, no… Oh, my God, Bones. Is that what you think I was doing?" He kissed her hand and then stated, "I was not with Hannah."

Turning her head to finally look him in the eye, she insisted, "I heard her voice, Booth. Are you going to deny that it was her that I heard over your phone?"

"No. That was her. However, we were not together."

"Then how…?"

"Oh, to hell with it…. Will you listen? Please?", he begged.

Taking a slow breath, she nodded.

"Do you remember that she wanted to have dinner that night?"

"Yes."

"We never had dinner. After I dropped you off, I got a phone call from Director Stark. I went to his office and my friend Danny Beck from the CIA was there. He had requested my help on an op in Afghanistan. Stark agreed and I had no choice. No one was to know what we were doing or where we were going. Even I wasn't told until we were in the air. I told them the only way I would go willingly was if they let me call you first. I only had a few minutes to call. I didn't want you to worry, but they wouldn't let me tell you any specific details…not that I knew any."

"What did you do while you were there?"

"Can we have that discussion at a later time? I promise to tell you everything, but when we are at home where it's more private."

"Why was Hannah there?"

"She finally got her transfer that she wanted to return to Afghanistan. She hopped the same military ride Danny and I were on. Once we landed, a cameraman picked her up. She went one way and Danny and I went the other. I swear."

She knew Booth well enough and knew he was being sincere. She was slowly losing her anger, but by this time, the stress of the last few weeks and this day were wearing on her. She found it too difficult to suppress her emotions any longer. Tears began to make trails down her cheeks. Booth took his thumb and wiped them away. She leaned her face into his hand and he sat down on the side of the bed.

"Come 'ere", he gently pulled her forward and held her while she cried. "I am so, so sorry, Bones." She wrapped both her arms around his neck as he encircled her waist. "I missed you", he whispered into her hair and kissed the top of her head.

After a couple of minutes, she pulled back and wiped at her eyes. Booth reached over and handed her some tissues.

"I missed you, too. I'm glad you're back."

"Me, too. That was a very long two weeks. The op wasn't supposed to take that long."

Trying not to look at him, she said, "You had quite a long time on the flight. Did you and Hannah talk?"

"We did", he said nodding. "I apologized to her."

Brennan peeked up and asked incredulously, "Why did you apologize?" and then she looked down again to wipe her eye.

Slipping his hand under her chin, he encouraged her to look at him. "I told her I was sorry because I shouldn't have allowed myself to even start a relationship with her. She was fun and I tried to make myself believe that I loved her. I guess in a way, I did on some level. But I confessed to her that you were the one I was trying to move on from when we met and that I should have known better. There is no moving on from you. When I proposed to her, I think deep down I knew she would say no and we would be over. I kind of forced her hand if you will. I also told her that we are together now and that I am happy."

"How did she respond to all of that?"

"Deep down, she understood; I think. I apologized for hurting her and we left it at that. I wished her luck and she said she was happy for the two of us."

"Are you happy, Booth?"

"Yea. I am happy. You make me happy, Bones."

Nodding her head, she looked down and then reached over to the bedside table and grabbed the piece of paper that she had been studying earlier.

"Booth, I have something I have to tell you."

"What's that?"

Nervously, she held out the paper to hand to him. When he looked at it, she swallowed and stated, "I…I'm pregnant."

Booth just stared at the sonogram picture. Brennan took his silence as disapproval and began to babble.

"I know we took precautions, and I hadn't planned on this. I don't want you to feel as if you have to…"

Booth looked up as she continued and finally decided that the only way she was going to stop was if he made her. So, he leaned forward and pressed his lips against hers. When he pulled back, she was still trying to talk, so he placed his hand on the back of her head and pulled her in for another kiss. This one was much more passionate and he tried to impress upon her how much he loved her at that moment. When the kiss ended, he rested their foreheads together and said, "Temperance Brennan…I love you so much."

"So, you're not mad about the baby?"

Smiling, he laughed and said, "Mad?! How could I possibly be upset that you are pregnant with my baby?"

"Really?"

"No, I am not mad. You have made me the happiest man in the world! I love you."

Tears began again to fall from her eyes.

"Wait. Are you okay with being pregnant? Do you want this baby?"

"Yes. Yes, Booth. I want this baby."

"Why didn't you tell me about it earlier?"

"I only found out that day that Hannah showed up at the dig site. I was going to tell you after you had dinner with Hannah."

"But, I had to leave."

"Yes."

"How far along are you?"

"About 8 and a half weeks. The fetus is approximately the size of a bean."

Wiping her tears away once more, he smiled and said, "There's something you need to know, too."

"What's that?"

"The doctor told me downstairs about the sonogram and the baby. I knew when I came up here."

"Why didn't you say anything?"

"Because, I wanted to hear about our baby from you. But, I'm not the only one that knows… Angela, Hodgins, and Cam were also standing with me. So, they now know there is an 'us' and there is a baby."

"Well, I guess that feline is no longer in the sack."

"Cat's out of the bag, Bones. Cat's out of the bag", he said laughing and shaking his head. Then he leaned in and kissed her again.

Author's note: I think I will leave our dynamic duo here. I was always disappointed that we never got to see Booth's reaction to Brennan's pregnancy announcement other than a smile at the end of season 6. I hope this has made an okay alternate story line. Thank you all for your kind remarks as you have read my thoughts. Here's to many more "BONES" stories.


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